sir,
I am studying the dynamics of membrane protein.I want to use amber force
field.Then what changes should I make in the ffnonbonded.itp and
ffbonded.itp?Is it similar as in Justin manual?Is it necessary to convert
C6 and C12 values in lipid.itp(for gromos) to values in terms of sigma and
epsi
Hello everyone:
I prepar to make a QM/MM simulation by employing gromacs compiled
with mopac, and need to define two groups which are treated by QM and MM
separately, the question is this: during the dynamics course of my research
system, particles will enter/leave the QM zone, so there is a
Standard procedure is to do
./configure
make
sudo make install
or
./configure --prefix=/somewhere/you/can/write/to
make
make install
I suggest you use sudo to get rid of your progress to date and start again.
Using sudo anywhere else is a recipe for trouble.
Mark
On Thu, Dec 27, 2012 at 3:41
On 27/12/12 16:29, vahid garshasbi wrote:
I run my simulation, now i want to analysis my data. i simulate ion
adsorption on CNT and i want to determine adsorption values in
deffrent concentrations of ion and then plot adsorpttion curve. what
shod i do?
Ask your advisor.
thanks, vahid
--
I will try to fix this. Thank you.
Now, the problem I have is that the executables all belong to root, and as
a user, I am unable to execute them. How to fix this little one?
Maria
On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham wrote:
> sudo should not be necessary for looking in those directori
sudo should not be necessary for looking in those directories. Whoever set
them up has not set up the permissions on them properly. Fix the problem,
not the symptoms - you do not want to have to configure software as root,
or you are trusting every author of that software not to trash your system
a
turned out to be a sudo problem. without sudo, the compiler could not look
into the root directories. sorry for spamming :(
On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic
wrote:
> Yes, I can see them in printenv
>
> does this have anything to do with single or double precision?
>
>
> On Thu, De
Maybe. As you will see in the installation instructions, you have to match
the precision of GROMACS and FFTW, and you haven't told us about the
former...
On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic
wrote:
> Yes, I can see them in printenv
>
> does this have anything to do with single or doub
Maria,
You can place the export command in your .profile. That will get them to work.
Use something like env | grep CPPFLAGS to make sure those settings are active
before compiling gromacs.
Best regards.
> Message: 6
> Date: Thu, 27 Dec 2012 11:31:10 +0100
> From: maria goranovic
> Subject: [gmx
Yes, I can see them in printenv
does this have anything to do with single or double precision?
On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham wrote:
> Are those variables actually showing up in your environment?
>
> On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic
> wrote:
>
> > Dear All
> >
> >
-- Forwarded message --
From: rama david
Date: Wed, Dec 26, 2012 at 9:55 PM
Subject: About g_enemat problem
To: gmx-users-ow...@gromacs.org
Hi Gromacs friend.
I simulated a system containing random peptide
I found that as they start to interact they change there secondary confor
Are those variables actually showing up in your environment?
On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic
wrote:
> Dear All
>
> I am trying to install 4.5.5 on my mac. I have installed fftw3 with
> --enable-float, and have used the CPPFLAGS and LDFLAGS options in my
> .bashrc file. GROMACS s
turns out that the command line tools were not installed by default in
xcode. installing them helped
On Tue, Dec 25, 2012 at 1:43 PM, Mark Abraham wrote:
> Unfortunately, it means what it says. Xcode by default does not install the
> command line compilers, so you might need to Google the solutio
Actually, merge.py takes care of it already. If you use that, the sed
command shouldn't be needed.
Did you perhaps mean updating the numbers of molecules in the topology? I
don't have an easy solution for that. Unless for the case where you have
1.gro/1.top and 2.gro/2.top, with all moleculetypes
14 matches
Mail list logo
